[gmx-users] free energy tutorial results

[David Mobley]

Yes, that's right.

Sorry for my obstinate choice of kcal/mol. Historical/lab reasons. I
should put a disclaimer on the page.

David


On 5/24/07, Jeroen van Bemmelen <J.J.M.vanBemmelen at tnw.tudelft.nl> wrote:
> Robert,
>
> Please check your units: GROMACS uses kJ/mol, while the tutorial uses
> kcal/mol, if I remember correctly. So there's a factor 4.2 between
> those two.
>
> Jeroen
>
>
> > Date: Thu, 24 May 2007 13:59:58 -0400
> > From: "Robert fiske" <rfiske_ at hotmail.com>
> > Subject: [gmx-users] free energy tutorial results
> > To: gmx-users at gromacs.org
> > Message-ID: <BAY118-F326F4F445CBD973E23896190340 at phx.gbl>
> > Content-Type: text/plain; format=flowed
> >
> > I am trying to follow the free energy tutorial by David. Mobley, however my
> > results are quite a bit off (after integration I get around -9.07) I have
> > only used lambda's spaced at 0,0.1,0.2,... but surely I should be much
> > closer than to the printed values of -2.18+/-0.01.  I am unsure if I am
> > making my mistake on the actual running of the free energy calculations
> > (since I've just copied and pasted my mdp files from the printed tutorial I
> > shouldn't have been able to screw that part up too much I would hope), the
> > only change I made was to set rlist and rcoulomb equal.  Or If I am messing
> > up in the data analysis part.  So this brings me to my question:
> >
> > Does anyone who has successfully run this tutorial have their dgdl.xvg files
> > from the individual runs (or the output from g_energy) so that I can see if
> > my simulations are correct, totally wrong, or if only a few lambda values
> > are off.
> >
> > Thank you for any assistance you can provide
> >
> > Robert Fiske
> > Gogonea Group
> > Cleveland Statue University
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